Summary: The latent thermal cationic initiators, benzyl‐2,5‐dimethylpyrazinium hexafluoroantimonate (BDPH) and benzyl‐2‐ethylpyrazinium hexafluoroantimonate (BEPH), were synthesized to investigate the effect of substituted alkyl groups on cure and dynamic mechanical behaviors of difunctional epoxy system. The cure temperature and activation energy of the diglycidyl ether of bisphenol A (DGEBA)/BDPH were higher than those of the DGEBA/BEPH, resulting from the steric hindrance of the substituted groups. The cross‐linking density of the DGEBA/BDPH was higher than that of the DGEBA/BEPH, whereas the Tg's of both specimens are similar. This may be explained by the free volume and the intermolecular hydrogen bonding induced by the hydrogen of the substituted methyl groups. Consequently, the position and number of the substituted groups of the latent thermal initiator were very important in the control of the latent thermal and dynamic mechanical behaviors of the epoxy resin.